Abstract：
BACKGROUND: This study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables.
METHODS: Twenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria.
RESULTS: Of 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree.
CONCLUSIONS: The bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.
METHODS: Twenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria.
RESULTS: Of 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree.
CONCLUSIONS: The bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.
摘要：
背景：这项研究描述了根尖周炎（AP）的原发性牙髓感染（PEI）的细菌群，确定了核心和稀有细菌组物种和群落多样性指标，并分析了细菌组成之间的关系，多样性和特点，和患者变量。
方法：对27例PEI和AP患者进行采样。提取DNA并使用qPCR定量。用DADA2流水线处理原始V3-V4扩增子测序数据以产生扩增子序列变体(ASV),并且针对HOMD进行了ASV直至物种水平的分类分配。使用ANCOM进行核心细菌组和差异丰度分析。使用Chao1，Shannon，和辛普森指数。LeFse分析用于鉴定丰富的分类单元。SECOM分析估计了细菌之间的线性和非线性关系。
结果：分析了24/27根管样本，和3个RCS以低读取计数滤出。平均相对丰度最高的细菌门是拟杆菌，Firmicutes,协同增效，镰刀菌,和放线菌.共鉴定出113属215种。将样品收集成三个簇。LeFse分析确定了不同年龄之间丰富分类群的差异，性别,症状学，和病变大小组。SECOM距离分析表明Slackiaexiguaas是程度最高的节点。
结论：本研究中的患者中，PEI伴AP的细菌组复杂，表现出高度的微生物异质性。此外，年龄,性别,症状学，和病变大小与PEI合并AP的细菌组特征差异相关。
方法：对27例PEI和AP患者进行采样。提取DNA并使用qPCR定量。用DADA2流水线处理原始V3-V4扩增子测序数据以产生扩增子序列变体(ASV),并且针对HOMD进行了ASV直至物种水平的分类分配。使用ANCOM进行核心细菌组和差异丰度分析。使用Chao1，Shannon，和辛普森指数。LeFse分析用于鉴定丰富的分类单元。SECOM分析估计了细菌之间的线性和非线性关系。
结果：分析了24/27根管样本，和3个RCS以低读取计数滤出。平均相对丰度最高的细菌门是拟杆菌，Firmicutes,协同增效，镰刀菌,和放线菌.共鉴定出113属215种。将样品收集成三个簇。LeFse分析确定了不同年龄之间丰富分类群的差异，性别,症状学，和病变大小组。SECOM距离分析表明Slackiaexiguaas是程度最高的节点。
结论：本研究中的患者中，PEI伴AP的细菌组复杂，表现出高度的微生物异质性。此外，年龄,性别,症状学，和病变大小与PEI合并AP的细菌组特征差异相关。
